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The Future of the Internet and its Impact on Digitally Enabled Genomic Medicine" Invited Talk InterWest Partners Menlo Park, CA May 2, 2005 Dr. Larry Smarr.

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Presentation on theme: "The Future of the Internet and its Impact on Digitally Enabled Genomic Medicine" Invited Talk InterWest Partners Menlo Park, CA May 2, 2005 Dr. Larry Smarr."— Presentation transcript:

1 The Future of the Internet and its Impact on Digitally Enabled Genomic Medicine" Invited Talk InterWest Partners Menlo Park, CA May 2, 2005 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technology Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD

2 Emergence of a Distributed Planetary Computer –Parallel Lambda Optical Backbone –Storage of Data Everywhere –Scalable Distributed Computing Power Wireless Access--Anywhere, Anytime –Broadband Speeds –Always Best Connected Billions of New Wireless Internet End Points –Information Appliances –Sensors and Actuators –Embedded Processors Transformational From Medicine to Transportation The Internet Is Extending Throughout the Physical World A Mobile Internet Powered by a Planetary Computer The all optical fibersphere in the center finds its complement in the wireless ethersphere on the edge of the network. --George Gilder

3 Where is Telecommunications Research Performed? A Historic Shift Source: Bob Lucky, Telcordia/SAIC U.S. Industry Non-U.S. Universities U.S. Universities Percent Of The Papers Published IEEE Transactions On Communications 70% 85%

4 Calit2 -- Research and Living Laboratories on the Future of the Internet UC San Diego & UC Irvine Faculty Working in Multidisciplinary Teams With Students, Industry, and the Community

5 Two New Calit2 Buildings Will Provide a Persistent Collaboration Living Laboratory Will Create New Laboratory Facilities –Nano, MEMS, RF, Optical, Visualization International Conferences and Testbeds Over 1000 Researchers in Two Buildings 150 Optical Fibers into UCSD Building Bioengineering UC San Diego UC Irvine California Provided $100M for Buildings Industry Partners $85M, Federal Grants $250M

6 Innovation Driven by Calit2 Industrial Partners Teaming with Academic Research and Education Funding Faculty Research Projects Supporting Graduate/Undergraduate Fellows Providing Access to Leading Edge Equipment Startups Integrated in Living Labs Joining on Federal Grants Co-Sponsoring Workshops/Conferences Hosting Seminars or Lectures Endowing Chaired Professorships

7 I Will Be Able to Cover Only a Fraction of the Calit2 Research Program Optical Networking and Biomedical Imaging Wireless Internet, BioMEMS, and Human Sensors Computational Biomedicine and Bioinformatics

8 Dedicated Optical Channels Makes High Performance Cyberinfrastructure Possible (WDM) Source: Steve Wallach, Chiaro Networks Lambdas Parallel Lambdas are Driving Optical Networking The Way Parallel Processors Drove 1990s Computing

9 From Supercomputer–Centric to Supernetwork-Centric Cyberinfrastructure Megabit/s Gigabit/s Terabit/s Network Data Source: Timothy Lance, President, NYSERNet 32x10Gb Lambdas 1 GFLOP Cray2 60 TFLOP Altix Bandwidth of NYSERNet Research Network Backbones T1 Optical WAN Research Bandwidth Has Grown Much Faster Than Supercomputer Speed! Computing Speed (GFLOPS)

10 Major Challenge for Data Intensive Science: Bandwidth Barriers Between User and Remote Resources National Partnership for Advanced Computational Infrastructure Part of the UCSD CRBS Center for Research on Biological Structure 10 Gbps Lambda Would Provide 200x Increase Average File Transfer ~10-50 Mbps Over Internet2 Backbone NIHs Biomedical Informatics Research Network

11 San Francisco Pittsburgh Cleveland NLR and TeraGrid Provides the Cyberinfrastructure Backbone for U.S. University Researchers San Diego Los Angeles Portland Seattle Pensacola Baton Rouge Houston San Antonio Las Cruces / El Paso Phoenix New York City Washington, DC Raleigh Jacksonville Dallas Tulsa Atlanta Kansas City Denver Ogden/ Salt Lake City Boise Albuquerque UC-TeraGrid UIC/NW-Starlight Chicago International Collaborators NLR 4 x 10Gb Lambdas Initially Capable of 40 x 10Gb wavelengths at Buildout NSFs TeraGrid Has 4 x 10Gb Lambda Backbone Links Two Dozen State and Regional Optical Networks DOE, NSF, & NASA Using NLR

12 Global Lambda Integrated Facility (GLIF) Integrated Research Lambda Network Many Countries are Interconnecting Optical Research Networks to form a Global SuperNetwork Visualization courtesy of Bob Patterson, NCSA Created in Reykjavik, Iceland 2003

13 September 26-30, 2005 University of California, San Diego California Institute for Telecommunications and Information Technology The Networking Double Header of the Century Will Be Driven by LambdaGrid Applications i Grid 2 oo 5 T H E G L O B A L L A M B D A I N T E G R A T E D F A C I L I T Y Maxine Brown, Tom DeFanti, Co-Organizers

14 The OptIPuter Project – Removing Bandwidth as an Obstacle In Data Intensive Sciences NSF Large Information Technology Research Proposal –Calit2 (UCSD, UCI) and UIC Lead CampusesLarry Smarr PI –Partnering Campuses: USC, SDSU, NW, TA&M, UvA, SARA, NASA Industrial Partners –IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent $13.5 Million Over Five Years Extending the Grid Middleware to Control Optical Circuits NIH Biomedical Informatics NSF EarthScope and ORION Research Network

15 The OptIPuter Project – Removing Bandwidth as an Obstacle In Data Intensive Sciences NSF Large Information Technology Research Proposal –Calit2 (UCSD, UCI) and UIC Lead CampusesLarry Smarr PI –Partnering Campuses: USC, SDSU, NW, TA&M, UvA, SARA, NASA Industrial Partners –IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent $13.5 Million Over Five Years Interactive Visualization of Remote Large Data Objects NIH Biomedical Informatics NSF EarthScope and ORION Research Network

16 Optical Networking, Internet Protocol, Computer Bringing the Power of Lambdas to Users Complete the Grid Paradigm by Extending Grid Middleware to Control Jitter-Free, Fixed Latency, Predictable Optical Circuits –One or Parallel Dedicated Light-Pipes –1 or 10 Gbps WAN Lambdas –Uses Internet Protocol, But Does NOT Require TCP –Exploring Both Intelligent Routers and Passive Switches Optical Circuits Plug Into User Linux Clusters Optimized for Storage, Visualization, or Computing –1 or 10 Gbps I/O per Node –Scalable Visualization Displays with OptIPuter Clusters

17 Realizing the Dream: High Resolution Portals to Global Science Data 650 Mpixel 2-Photon Microscopy Montage of HeLa Cultured Cancer Cells Green: Actin Red: Microtubles Light Blue: DNA Source: Mark Ellisman, David Lee, Jason Leigh, Tom Deerinck

18 OptIPuter LambdaVision Scalable Displays Being Developed for Multi-Scale Biomedical Imaging Green: Purkinje Cells Red: Glial Cells Light Blue: Nuclear DNA Source: Mark Ellisman, David Lee, Jason Leigh Two-Photon Laser Confocal Microscope Montage of 40x36=1440 Images in 3 Channels of a Mid-Sagittal Section of Rat Cerebellum Acquired Over an 8-hour Period 300 MPixel Image!

19 Scalable Displays Allow Both Global Content and Fine Detail Source: Mark Ellisman, David Lee, Jason Leigh 30 MPixel SunScreen Display Driven by a 20-node Sun Opteron Visualization Cluster

20 Allows for Interactive Zooming from Cerebellum to Individual Neurons Source: Mark Ellisman, David Lee, Jason Leigh

21 Toward an Interactive Gigapixel Display Scalable Adaptive Graphics Environment (SAGE) Controls: 100 Megapixels Display –55-Panel 1/4 TeraFLOP –Driven by 30-Node Cluster of 64-bit Dual Opterons 1/3 Terabit/sec I/O –30 x 10GE interfaces –Linked to OptIPuter 1/8 TB RAM 60 TB Disk Source: Jason Leigh, Tom DeFanti, EVL@UIC OptIPuter Co-PIs NSF LambdaVision MRI@UIC Calit2 is Building a LambdaVision Wall in Each of the UCI & UCSD Buildings

22 Campuses Must Provide Fiber Infrastructure to End-User Laboratories & Large Rotating Data Stores SIO Ocean Supercomputer IBM Storage Cluster 2 Ten Gbps Campus Lambda Raceway Streaming Microscope Source: Phil Papadopoulos, SDSC, Calit2 UCSD Campus LambdaStore Architecture Global LambdaGrid

23 The Optical Core of the UCSD Campus-Scale Testbed -- Evaluating Packet Routing versus Lambda Switching Goals by 2007: >= 50 endpoints at 10 GigE >= 32 Packet switched >= 32 Switched wavelengths >= 300 Connected endpoints Approximately 0.5 TBit/s Arrive at the Optical Center of Campus Switching will be a Hybrid Combination of: Packet, Lambda, Circuit -- OOO and Packet Switches Already in Place Source: Phil Papadopoulos, SDSC, Calit2 Funded by NSF MRI Grant Lucent Glimmerglass Chiaro Networks

24 OptIPuter Middleware Architecture-- The Challenge of Transforming Grids into LambdaGrids Distributed Applications/ Web Services Telescience GTPXCPUDT LambdaStream CEPRBUDP Vol-a-Tile SAGEJuxtaView Visualization DVC Configuration DVC API DVC Runtime Library Data Services LambdaRAM Globus XIO PIN/PDC DVC Services DVC Core Services DVC Job Scheduling DVC Communication Resource Identify/Acquire Namespace Management Security Management High Speed Communication Storage Services GRAM GSI RobuStore Photonic Infrastructure

25 UCSD StarLight Chicago UIC EVL NU CENIC San Diego GigaPOP CalREN-XD 8 8 The OptIPuter LambdaGrid is Rapidly Expanding NetherLight Amsterdam U Amsterdam NASA Ames NASA Goddard NLR 2 SDSU CICESE via CUDI CENIC/Abilene Shared Network 1 GE Lambda 10 GE Lambda PNWGP Seattle CAVEwave/NLR NASA JPL ISI UCI CENIC Los Angeles GigaPOP 2 2 Source: Greg Hidley, Aaron Chin, Calit2

26 Multiple HD Streams Over Lambdas Will Radically Transform Global Collaboration U. Washington JGN II Workshop Osaka, Japan Jan 2005 Prof. Osaka Prof. Aoyama Prof. Smarr Source: U Washington Research Channel Telepresence Using Uncompressed 1.5 Gbps HDTV Streaming Over IP on Fiber Optics-- 75x Home Cable HDTV Bandwidth!

27 Brain Imaging Collaboration -- UCSD & Osaka Univ. Using Real-Time Instrument Steering and HDTV Southern California OptIPuter Most Powerful Electron Microscope in the World -- Osaka, Japan Source: Mark Ellisman, UCSD UCSD HDTV

28 Digitally Enabled Animal Observation: Mouse Tracking in Calit2 Smart Vivarium Capture and Process Continuous Video Observing Mice –Scalable to Thousands of Cages Maintain Health and Welfare & Perform Biomedical Experiments –How Far Does Each Mouse Run in a Day? –Behaviour Tracking (Sitting, Running, Grooming, Feeding) Integrated System –Computer Vision –Pattern Recognition –Embedded Systems –Distributed Computation Gigabytes/s of Video Data => Petabytes in Archives mean covariance Source: Serge Belongie, CSE UCSD

29 An Explosion in Wireless Internet Connectivity is Occuring Distance/Topology/Segments CBD/Dense Urban Industrial Suburban Residential Suburban Rural 10Gbps 1 Gbps 100 Mbps 10 Mbps Short <1km Short/Medium 1- 2km Medium 2-5 km Medium/Long >5 km Long >10 km 802.11 a/b/g Point to Point Microwave $2B-$3B/Year Fiber – Multi-billion $ E-Band Market Opportunity $1B+ Market Demand 802.16 Wi-Max FSO & 60GHz Radio ~$300M $2-$4B in 5 years Broadband Cellular Internet Plus…

30 The Calit2@UCSD Building Was Designed for the Wireless Age Nine Antenna Pedestals on Roof –Can Support Ericssons Latest Compact Base Station –Or Antennas for a Macro Base Station Rooftop Research Shack –Vector Network Analyzers –Spectrum Analyzers –CDMA Air Interface Software Test Tools Dedicated Fiber Optic and RF connections Between Labs Network of Interconnected Labs –Antenna Garden, e.g. Roof Top –Radio Base Station Lab, e.g. 6 th floor –Radio Network Controller Lab, e.g. 5 th floor –Always Best Connected & LocatedThroughout Building GPS Re-Radiators in Labs –Distribution of Timing Signals Building Materials Were Chosen To Maximize Radio Penetration

31 The CWC Provides Calit2 With Deep Research in Many Component Areas Two Dozen ECE and CSE Faculty LOW-POWERED CIRCUITRY ANTENNAS AND PROPAGATION COMMUNICATION THEORY COMMUNICATION NETWORKS MULTIMEDIA APPLICATIONS RF Mixed A/D ASIC Materials Smart Antennas Adaptive Arrays Modulation Channel Coding Multiple Access Compression Architecture Media Access Scheduling End-to-End QoS Hand-Off Changing Environment Protocols Multi-Resolution Center for Wireless Communications Source: UCSD CWC

32 The Center for Pervasive Communications and Computing Will Have a Major Presence in the Calit2@UCI Building Director Ender Ayanoglu Over 20 Affiliated Faculty

33 Network Endpoints Are Becoming Complex Systems-on-Chip Two Trends: More Use of Chips with Embedded Intelligence Networking of These Chips Source: Rajesh Gupta, UCSD Director, Center for Microsystems Engineering Calit2 Has Created Nano/ MEMS Clean Rooms, RF, Embedded Processor & System-on-Chip Labs

34 The UCSD Program in Embedded Systems & Software Confluence of: –Architecture, Compilers –VLSI, CAD, Test –Embedded Software Cross-Cutting Research Thrusts: –Low Power, Reliability, Security –Sensor Networks Affiliated Laboratories: –High Performance Processor Architecture and Compiler –Microelectronic Systems Lab VLSI/CAD Lab –Reliable System Synthesis Lab Calit2 MicroSystems Engineering Initiative

35 UC Irvine Integrated Nanoscale Research Facility – Materials and Devices Collaboration with Industry Collaborations with Industry –Joint Research With Faculty –Shared Facility Available For Industry Use $1M $2M $3M $4M $5M 99-0000-01 01-0202-03 Federal agencies Industry partners State funding Private foundations Working with UCI OTA to Facilitate Tech Transfer Industry and VC Interest in Technologies Developed at INRF Research Funding Equipment Funding

36 UCI Has Built a World Class Multi-Departmental BioMEMS Faculty Developing BioMEMS –Mark Bachman (EECS) –Peter Burke (EECS) –Noo Li Jeon (BME) –John LaRue (MAE) –Abe Lee (BME) –G.P. Li (EECS) –Marc Madou (MAE) –Rick Nelson (EECS) –Andrei Shkel (MAE) –Bill Tang (BME) Using BioMEMS –Nancy Allbritton (MED) –Zhongping Chen (BME) –BME faculty –Many in College of Medicine Orange County has the Largest Concentration of Biomedical Device Industry San Diego has the 3rd Largest Concentration of Biotech Industry Henry Samueli School of Engineering

37 Research Topics of INRF / Calit2@UCI BioMEMS Team Micro Resonators for Wireless Communications Optical Coherence Tomography Mechanosensitivity Microplatforms Micro- and Nano- Fluidics Protein Crystallization in Nanovolumes Nano-Biosensors Catheter-Based Microtools Silicon-Based HF Ultrasonic Atomizers Smart Pills Bionic Ear

38 Guided wave optics Aqueous bio/chem sensors Fluidic circuit Free space optics Physical sensors Gas/chemical sensors Electronics (communication, powering) I. K. Schuller holding the first prototype I. K. Schuller, A. Kummel, M. Sailor, W. Trogler, Y-H Lo Integrated Nanosensors Collaborative Research Between Physicists, Chemists, Material Scientists and Engineers Developing Multiple Nanosensors on a Single Chip, with Local Processing and Wireless Communications

39 UCSD Optofluidics Faculty are Working Toward Photonic Integrated Information Systems VCSEL + Near-field polarizer : Efficient polarization control,mode stabilization, and heat management Composite nonlinear, E-O, and artificial dielectric materials control and enhance near-field coupling Near-field coupling between pixels in Form-birefringent CGH FBCGH possesses dual-functionality such as focusing and beam steering Wavelength ( m) Reflectivity 0.0 0.2 0.4 0.6 0.8 1.0 TE TM Information I/O through surface wave, guided wave,and optical fiber from near-field edge and surface coupling Near-field E-O modulator controls optical properties and near-field micro-cavity enhances the effect +V -V Angle (degree) 203040 TM Efficiency 0.0 0.2 0.4 0.6 0.8 1.0 Near-field E-O Modulator + micro-cavity FBCGH VCSEL Near-field E-O coupler Micro polarizer Fiber tip Grating coupler Thickness ( m) 0.600.650.700.750.80 TM 0th order efficiency 0.2 0.4 0.6 0.8 1.0 RCWA Transparency Theory Near-field coupling -fluidic integrated systems Form-birefringent Polarization splitter Multicavity resonant delay line Composite, nonlinear, E-O, and artificial dielectric materials control and enhance near- field coupling Form birefringent WG & pol-rotator Ultrashort pulses in Photonic Crystals TM-Transmitted TE-Reflected Electrical, Optical, Fluidic, Magnetic, Mechanical, Acoustic, Chemical, & Biological Signals and Processes on a Chip

40 Wireless Internet Information System for Medical Response in Disasters (WIISARD) First Responder Wireless Location Aware Systems For Nuclear, Chemical & Radiologic Attacks –Total NIH Award: $4.1 Million. –Duration 10/03 To 10/06 WIISARD Drill 3/16/04 Leslie Lenert, PI, UCSD SOM Leslie Lenert, PI UCSD SOM

41 Current Information Management Tools for Mass Casualty Events are Pre-Digital Disaster Triage Tags 800 mHz Shared Radios Felt Pen/Whiteboard Fire Trucks and Chalk!

42 Calit2 Cybershuttle Operations Base for Disaster Drills With Rapid Setup Wireless Mesh Network Self Configuring Mesh Network with Multiple Access Points that Aggregate Uplink Bandwidth with Auto-Reconfiguration and Fail-Over

43 Wireless Video Transmission Capability Major Improvement for Hazmat and Medical Units

44 Calit2 Prototype--Active RFID Triage Tag Built on WiFi Embedded Systems Technologies Build from Commercial Components –Dpac WiFi Module –Ubicom Application and Web Server Processor –Rapid Association with Network and Battery Conservation Cycle TCP/IP Communications –Heart Beat + Geolocation –Receives Instructions from Command Center Systems & Responds –Displays Triage Status & Alerts With LEDs –Stores Medical Data in Flash ROM for Offsite Access +

45 Embedded Systems WiFi Pulse Oximeter: Low Cost Improved Aid Stations Nellcor MP100 OEM Pulse Oximetry Board Windows XP Monitoring App Waterproof Case With LCD/LED WiFi Module Nellcor Forehead O2 Sensor

46 First Tier Provider Handheld WiFi Systems Tactical Maps and Communications Triage and Care Linux OS

47 Calit2 is Collaborating with UCSD and UCI as They Design Smart Hospitals The new UCI medical center will be a smart hospital, utilizing the latest telecommunications, automation and Internet developments to elevate patient care, teaching and research to a new level. Wired and wireless technology will improve and expedite communications among all members of a patients medical team, enabling critical patient data and test results to be transmitted immediately to all members. Additionally, the latest technology will enhance ultrasound, communications, security, computer networking, closed-network television and the dispensing of pharmaceuticals. To be Completed in Late 2008 Calit2 Testbed in UCSD/VA iTech Discussing Collaborations with Mayo, IBM, NIH, Navy

48 Calit2 Brings Computer Scientists and Mathematicians Together with Biomedical Researchers Some Areas of Concentration: –Genomic Analysis of Organisms –Evolution of Genomes –Cancer Genomics –Human Genomic Variation and Disease –Mitochondrial Evolution –Proteomics –Computational Biology –Information Theory and Biological Systems

49 Comparative Genomics Utilizes Advanced Algorithmic Techniques After sequencing these three genomes, it is clear that substantial rearrangements in the human genome happen only once in a million years, while the rate of rearrangements in the rat and mouse is much faster. --Glenn Tesler, UCSD Dept. of Mathematics Co-Authors Pavel Pevzner and Glenn Tesler, UCSD April 1, 2004 December 05, 2002 December 9, 2004

50 Evolution is the Principle of Biological Systems: Computational Techniques are Critical for Discovery Many of the chicken– human aligned, non-coding sequences occur far from genes, frequently in clusters that seem to be under selection for functions that are not yet understood. Nature 432, 695 - 716 (09 December 2004)

51 Algorithms for Untangling Genome Rearrangements are Critical to Understanding Genetic Evolution Pevzner & Tesler Derived the Multi-Chromosomal Rearrangement Scenaria for Entire Human-Mouse Genomes –Nature, 2002, Genome Research, 2003 What are the Architectural Blocks Forming the Existing Genomes? –How Do We Find Them? –What is the Evolutionary Scenario for Transforming One Genome into the Other? Source: Pavel Pevzner, UCSD

52 Evolutionary Genomic Rearrangements are Central to Cancer Genomics Change Gene Structure & Regulatory Wiring of the Genome Create Bad Novel Fusion Genes & Break Good Old Genes Example: –Translocation In Leukemia –e.g. Gleevec TM (Novartis 2001) Targets BCR-ABL Oncogene promoter ABL gene BCR genepromoter Chromosome 9 Chromosome 22 BCR-ABL oncogene Source: Pavel Pevzner and Ben Raphael, Computer Science, UCSD; Colin Collins lab at UCSF Cancer Center

53 Toward Digitally Enabled Genetic Medicine: Statistical Analysis of Human Genetic Variation The structure of human populations is relevant in various epidemiological contexts. As a result of variation in frequencies of both genetic and non-genetic risk factors, rates of disease and of such phenotypes as adverse drug response vary across populations. Further, information about a patient's population of origin might provide health-care practitioners with information about risk when direct causes of disease are unknown. --Genetic Structure of Human Populations Rosenberg, et al. Science 298: 2381-2385 (2002)

54 The Phylogeography of Y Chromosome Binary Haplotypes and the Origins of Modern Human Populations Underhill, et al. Ann. Hum. Genet. (2001) 65: 43-62 1062 Men from 21 Populations 218 Polymorphisms from NRY

55 The Private Sector is Becoming an Essential Partner in Genomics

56 David A. Hinds, Laura L. Stuve, Geoffrey B. Nilsen, Eran Halperin, Eleazar Eskin, Dennis G. Ballinger, Kelly A. Frazer, David R. Cox. Whole-Genome Patterns of Common DNA Variation in Three Human Populations Science 18 February, 2005: 307(5712):1072-1079. Calit2 Researcher Eskin Collaborates with Perlegen Sciences on Map of Human Genetic Variation Across Populations We have characterized whole-genome patterns of common human DNA variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) in 71 Americans of European, African, and Asian ancestry. Although knowledge of a single genetic risk factor can seldom be used to predict the treatment outcome of a common disease, knowledge of a large fraction of all the major genetic risk factors contributing to a treatment response or common disease could have immediate utility, allowing existing treatment options to be matched to individual patients without requiring additional knowledge of the mechanisms by which the genetic differences lead to different outcomes. More detailed haplotype analysis results are available at

57 Calit2 is Collaborating with Doug Wallace Planning to Bring MITOMAP into Calit2 Domain The Human mtDNA Map, Showing the Location of Selected Pathogenic Mutations Within the 16,569-Base Pair Genome MITOMAP: A Human Mitochondrial Genome Database., 2005 5 March 1999

58 For Mitochondrial Diseases It Has Been More Productive to Classify Patients by Genetic Defect Rather than by Clinical Manifestation Over the past 10 years, mitochondrial defects have been implicated in a wide variety of degenerative diseases, aging, and cancer… The same mtDNA mutation can produce quite different phenotypes, and different mutations can produce similar phenotypes. …The essential role of mitochondrial oxidative phosphorylation in cellular energy production, the generation of reactive oxygen species, and the initiation of apoptosis has suggested a number of novel mechanisms for mitochondrial pathology. --Douglas Wallace, Science, Vol. 283, 1482-1488, 5 March 1999

59 The Protein Data Bank Personnel Supported by SDSC Will Be Housed in the new Calit2@UCSD Building The Single International Repository for 3-D Structure Data of Biological Macro-molecules (Over 30,000 Structures) More Than 160,000 Web Hits Per Day

60 The Bioinformatics Core of the Joint Center for Structural Genomics will be Housed in the Calit2@UCSD Building The Bioinformatics Core (BIC) is Responsible for: (1)Target Selection; (2) Sample Tracking; (3) Information Management; (4) Structure Validation; (5) Deposition; And (6) Post-structural Analysis.

61 Determining the Protein Structures of the Thermophilic Thermotoga Maritima GenomeLife at 80 o C! Extremely Thermostable -- Useful for Many Industrial Processes (e.g. Chemical and Food) 173 Structures (122 from JCSG) 122 T.M. Structures Solved by JCSG (75 Unique In The PDB) Direct Structural Coverage of 25% of the Expressed Soluble Proteins Probably Represents the Highest Structural Coverage of Any Organism Source: John Wooley, UCSD

62 UCIs IGB Develops a Suite of Programs and Servers for Protein Structure and Structural Feature Prediction Source: Pierre Baldi, UCI Sixty Affiliated IGB Labs at UCI e.g.:

63 Web PortalRich Clients Providing Integrated Grid Software and Infrastructure for Multi-Scale BioModeling Telescience Portal Grid Middleware and Web Services Workflow Middleware PMV ADT Vision Continuity APBSCommand Grid and Cluster Computing ApplicationsInfrastructure Rocks Grid of Clusters APBS Continuity Gtomo2 TxBR Autodock GAMESS QMView National Biomedical Computation Resource an NIH supported resource center Located in Calit2@UCSD Building

64 Information Theorists Working with Biologists and Computer Scientists Will Radically Transform Our View of Living Systems "Through the strong loupe of information theory, we will be able to watch how such [living] beings do what nonliving systems cannot do: extract information from their surrounds, store it is a stable molecular form, and eventually parcel it out for their creative endeavors.... So viewed, the information circle becomes the unit of life. --Werner Loewenstein The Touchstone of Life (1999) Calit2@UCSD Will House One of the Worlds Best Information Theory Groups Toby Berger IEEE Shannon Award 2002 Living Systems are Shannon-Optimum Without Coding

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